class=$1

################################### MutSig2CV 编码区
#################
## 1、合并MAF
sh ${scripts_path}/mutsig/Mutsig_1_Combine-maf.MSI.sh ${class}

#################
## 2、跑Mutsig2CV
#### 提取需要的列，可以加速突变导入速度
## 5:Chromosome
## 6:Start_position
## 16:Tumor_Sample_Barcode
## 11:Reference_Allele
## 13:Tumor_Seq_Allele2
## 1:Hugo_Symbol
## 9:Variant_Classification
## 10:Variant_Type
## 同一个人同一位置突变算1个
cat ${maf_path}/All_ForMutSig.${class}.MSI.maf | \
awk -F'\t' '{OFS="\t"}{print $5,$6,$16,$11,$13,$1,$9,$10}' | head -1 > ${maf_path}/All_ForMutSig.extract.${class}.MSI.maf
cat ${maf_path}/All_ForMutSig.${class}.MSI.maf | grep -v Chromosome | \
awk -F'\t' '{OFS="\t"}{print $5,$6,$16,$11,$13,$1,$9,$10}' | sort -u >> ${maf_path}/All_ForMutSig.extract.${class}.MSI.maf
